Background: The Repeat Expansion Diseases are caused by the intergenerational expansion of a specific tandem repeat. GAATTC-repeat expansion in the first intron of the frataxin gene results in a transcription defect that leads to a deficit of frataxin, a protein involved in mitochondrial iron homeostasis. This results in Friedreich ataxia (FRDA), a relentlessly progressive neurodegenerative disease. In addition to the consequences of cerebellar degeneration, FRDA symptoms include diabetes and a frequently fatal hypertrophic cardiomyopathy. Thus the frataxin deficit has consequences outside of the CNS as well. How an intronic repeat affects gene expression is unknown. Previous work from this workgroup and elsewhere revealed one potential way in which repeat expansion in the intron could produce an mRNA deficit. We showed that in vitro the repeat was able to form a triple-stranded DNA structure (triplex) that trapped the RNA polymerase on the template (Grabczyk and Usdin, 2000 a,b). However, whether such a triplex forms in the endogenous frataxin locus in vivo is unknown.[unreadable] [unreadable] Progress report: We have shown that the GAATTC-repeat expansion responsible for FRDA causes the flanking sequence to become aberrantly methylated (Greene et. al., 2007). Not only does the basal level of methylation present in this region extend further 5 of the repeat, but some residues that are rarely, if ever, methylated in cells from unaffected individuals, become heavily methylated in patient cells. The hypomethylated residues in unaffected individuals resemble a naturally occurring methylation footprint where DNA binding proteins protect bases within their binding site from methylation. We have shown that one of the methylation footprints corresponds to a transcription factor binding site. Deletion of this binding site leads to a significant reduction in the activity of a reporter construct in muscle cells. The absence of such a footprint in patients suggests that the expanded repeats may alter the chromatin in this region making the DNA less accessible for protein binding. The net result would be reduced frataxin transcription. We have found elevated levels of histone H3 dimethylated at lysine 9 (H3K9Me2) on the frataxin gene in FRDA cells that would be consistent with such a model (Greene et. al., 2007). [unreadable] [unreadable] Our results have some important implications. Firstly, the epigenetic changes on the FRDA alleles are reminiscent of the gene silencing responsible for another Repeat Expansion Disease, Fragile X mental retardation syndrome (FXS). FXS results from expansion of a different repeat that is also normally transcribed but not translated. This suggests that the underlying mechanism for repeat mediated gene silencing in these 2 disorders may be more similar than originally anticipated. It also raises the possibility that similar approaches may be useful in ameliorating disease symptoms in both disorders. Furthermore, our data suggest that DNA methylation is secondary to other epigenetic changes in the FRDA locus and, since the FRDA repeat contains no CpG residues, the repeat cannot be the nidus for DNA methylation as originally suggested for the FXS repeats. Thus it may be that the trigger for DNA methylation in both FRDA and FXS lies elsewhere and that a different common mechanism may be responsible for not only these 2 diseases but other Repeat Expansion Diseases where the repeat is transcribed.